Job ID = 5790778 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,792,082 reads read : 37,584,164 reads written : 18,792,082 reads 0-length : 18,792,082 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:14:08 18792082 reads; of these: 18792082 (100.00%) were unpaired; of these: 4645919 (24.72%) aligned 0 times 10135852 (53.94%) aligned exactly 1 time 4010311 (21.34%) aligned >1 times 75.28% overall alignment rate Time searching: 00:14:10 Overall time: 00:14:10 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1130980 / 14146163 = 0.0799 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 07:21:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625152/SRX7625152.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625152/SRX7625152.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625152/SRX7625152.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625152/SRX7625152.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Apr 2020 07:21:45: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:21:45: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:21:53: 1000000 INFO @ Wed, 22 Apr 2020 07:22:01: 2000000 INFO @ Wed, 22 Apr 2020 07:22:09: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 07:22:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625152/SRX7625152.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625152/SRX7625152.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625152/SRX7625152.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625152/SRX7625152.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Apr 2020 07:22:13: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:22:13: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:22:17: 4000000 INFO @ Wed, 22 Apr 2020 07:22:22: 1000000 INFO @ Wed, 22 Apr 2020 07:22:25: 5000000 INFO @ Wed, 22 Apr 2020 07:22:30: 2000000 INFO @ Wed, 22 Apr 2020 07:22:34: 6000000 INFO @ Wed, 22 Apr 2020 07:22:39: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 07:22:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625152/SRX7625152.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625152/SRX7625152.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625152/SRX7625152.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625152/SRX7625152.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Apr 2020 07:22:43: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:22:43: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:22:43: 7000000 INFO @ Wed, 22 Apr 2020 07:22:47: 4000000 INFO @ Wed, 22 Apr 2020 07:22:51: 1000000 INFO @ Wed, 22 Apr 2020 07:22:52: 8000000 INFO @ Wed, 22 Apr 2020 07:22:56: 5000000 INFO @ Wed, 22 Apr 2020 07:23:00: 2000000 INFO @ Wed, 22 Apr 2020 07:23:01: 9000000 INFO @ Wed, 22 Apr 2020 07:23:05: 6000000 INFO @ Wed, 22 Apr 2020 07:23:08: 3000000 INFO @ Wed, 22 Apr 2020 07:23:10: 10000000 INFO @ Wed, 22 Apr 2020 07:23:14: 7000000 INFO @ Wed, 22 Apr 2020 07:23:16: 4000000 INFO @ Wed, 22 Apr 2020 07:23:19: 11000000 INFO @ Wed, 22 Apr 2020 07:23:22: 8000000 INFO @ Wed, 22 Apr 2020 07:23:24: 5000000 INFO @ Wed, 22 Apr 2020 07:23:28: 12000000 INFO @ Wed, 22 Apr 2020 07:23:31: 9000000 INFO @ Wed, 22 Apr 2020 07:23:33: 6000000 INFO @ Wed, 22 Apr 2020 07:23:38: 13000000 INFO @ Wed, 22 Apr 2020 07:23:38: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:23:38: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:23:38: #1 total tags in treatment: 13015183 INFO @ Wed, 22 Apr 2020 07:23:38: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:23:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:23:38: #1 tags after filtering in treatment: 13015008 INFO @ Wed, 22 Apr 2020 07:23:38: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:23:38: #1 finished! INFO @ Wed, 22 Apr 2020 07:23:38: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:23:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:23:39: #2 number of paired peaks: 5787 INFO @ Wed, 22 Apr 2020 07:23:39: start model_add_line... INFO @ Wed, 22 Apr 2020 07:23:39: 10000000 INFO @ Wed, 22 Apr 2020 07:23:39: start X-correlation... INFO @ Wed, 22 Apr 2020 07:23:39: end of X-cor INFO @ Wed, 22 Apr 2020 07:23:39: #2 finished! INFO @ Wed, 22 Apr 2020 07:23:39: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Apr 2020 07:23:39: #2 alternative fragment length(s) may be 74,526,593 bps INFO @ Wed, 22 Apr 2020 07:23:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625152/SRX7625152.05_model.r WARNING @ Wed, 22 Apr 2020 07:23:39: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:23:39: #2 You may need to consider one of the other alternative d(s): 74,526,593 WARNING @ Wed, 22 Apr 2020 07:23:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:23:39: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:23:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:23:41: 7000000 INFO @ Wed, 22 Apr 2020 07:23:48: 11000000 INFO @ Wed, 22 Apr 2020 07:23:50: 8000000 INFO @ Wed, 22 Apr 2020 07:23:56: 12000000 INFO @ Wed, 22 Apr 2020 07:23:58: 9000000 INFO @ Wed, 22 Apr 2020 07:24:05: 13000000 INFO @ Wed, 22 Apr 2020 07:24:05: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:24:05: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:24:05: #1 total tags in treatment: 13015183 INFO @ Wed, 22 Apr 2020 07:24:05: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:24:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:24:05: #1 tags after filtering in treatment: 13015008 INFO @ Wed, 22 Apr 2020 07:24:05: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:24:05: #1 finished! INFO @ Wed, 22 Apr 2020 07:24:05: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:24:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:24:06: 10000000 INFO @ Wed, 22 Apr 2020 07:24:07: #2 number of paired peaks: 5787 INFO @ Wed, 22 Apr 2020 07:24:07: start model_add_line... INFO @ Wed, 22 Apr 2020 07:24:07: start X-correlation... INFO @ Wed, 22 Apr 2020 07:24:07: end of X-cor INFO @ Wed, 22 Apr 2020 07:24:07: #2 finished! INFO @ Wed, 22 Apr 2020 07:24:07: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Apr 2020 07:24:07: #2 alternative fragment length(s) may be 74,526,593 bps INFO @ Wed, 22 Apr 2020 07:24:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625152/SRX7625152.10_model.r WARNING @ Wed, 22 Apr 2020 07:24:07: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:24:07: #2 You may need to consider one of the other alternative d(s): 74,526,593 WARNING @ Wed, 22 Apr 2020 07:24:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:24:07: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:24:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:24:09: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:24:14: 11000000 INFO @ Wed, 22 Apr 2020 07:24:21: 12000000 INFO @ Wed, 22 Apr 2020 07:24:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625152/SRX7625152.05_peaks.xls INFO @ Wed, 22 Apr 2020 07:24:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625152/SRX7625152.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:24:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625152/SRX7625152.05_summits.bed INFO @ Wed, 22 Apr 2020 07:24:23: Done! pass1 - making usageList (65 chroms): 0 millis pass2 - checking and writing primary data (1008 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:24:29: 13000000 INFO @ Wed, 22 Apr 2020 07:24:30: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:24:30: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:24:30: #1 total tags in treatment: 13015183 INFO @ Wed, 22 Apr 2020 07:24:30: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:24:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:24:30: #1 tags after filtering in treatment: 13015008 INFO @ Wed, 22 Apr 2020 07:24:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:24:30: #1 finished! INFO @ Wed, 22 Apr 2020 07:24:30: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:24:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:24:31: #2 number of paired peaks: 5787 INFO @ Wed, 22 Apr 2020 07:24:31: start model_add_line... INFO @ Wed, 22 Apr 2020 07:24:31: start X-correlation... INFO @ Wed, 22 Apr 2020 07:24:31: end of X-cor INFO @ Wed, 22 Apr 2020 07:24:31: #2 finished! INFO @ Wed, 22 Apr 2020 07:24:31: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Apr 2020 07:24:31: #2 alternative fragment length(s) may be 74,526,593 bps INFO @ Wed, 22 Apr 2020 07:24:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625152/SRX7625152.20_model.r WARNING @ Wed, 22 Apr 2020 07:24:31: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:24:31: #2 You may need to consider one of the other alternative d(s): 74,526,593 WARNING @ Wed, 22 Apr 2020 07:24:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:24:31: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:24:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:24:36: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:24:51: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625152/SRX7625152.10_peaks.xls INFO @ Wed, 22 Apr 2020 07:24:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625152/SRX7625152.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:24:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625152/SRX7625152.10_summits.bed INFO @ Wed, 22 Apr 2020 07:24:51: Done! pass1 - making usageList (55 chroms): 0 millis pass2 - checking and writing primary data (637 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:24:59: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:25:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625152/SRX7625152.20_peaks.xls INFO @ Wed, 22 Apr 2020 07:25:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625152/SRX7625152.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:25:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625152/SRX7625152.20_summits.bed INFO @ Wed, 22 Apr 2020 07:25:14: Done! pass1 - making usageList (41 chroms): 0 millis pass2 - checking and writing primary data (345 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。